[Bioperl-l] Batch retrieval partially implemented inBio::DB::GenBank/GenPept

[Chris Fields]

> -----Original Message-----
> From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-
> bounces at lists.open-bio.org] On Behalf Of Chris Fields
> Sent: Wednesday, May 03, 2006 4:10 PM
> To: 'Jason Stajich'; 'Brian Osborne'; bioperl-l at lists.open-bio.org
> Subject: [Bioperl-l] Batch retrieval partially implemented
> inBio::DB::GenBank/GenPept
> 
> Just wanted to let you guys know I have added a few bits and pieces to
> Bio::DB::Gen*  and BioLLDB::NCBIHelper for batch retrieval using
                     ^^^^^^^^^^^^^^^^^^^
                     Bio::DB::NCBIHelper
Fat fingers!

> epost/efetch.  I didn't want to break anything too severely so you can
> only
> use this at the moment using get_seq_stream (i.e. NOT through get_Stream*
> methods yet).  I also added tests to DB.t, a few each for protein and
> nucleotide retrieval using batch mode and so far they all pass fine.
> 
> I haven't tested the upper sequence limit for this yet to see if it's at
> all
> comparable to just using efetch but it seems a bit faster.  The eutils
> coursebook states that one should only post ~500 at a time (I think you
> can
> get a bit higher though).
> 
> Also, at the moment it only works at the moment for GI's (NOT accessions,
> which apparently epost does not accept).  If we want to continue using
> this
> method for retrieval then we may need a workaround for accs.
> 
> CJF
> 
> Christopher Fields
> Postdoctoral Researcher - Switzer Lab
> Dept. of Biochemistry
> University of Illinois Urbana-Champaign
> 
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l